Strain selection of pneumococcal surface proteins

ABSTRACT

The present invention relates to vaccine composition(s) comprising at least two PspAs from strains selected from at least one family, the family being defined by PspAs from strains belonging to the family having greater than or equal to 50% homology in aligned sequences of a C-terminal region of an alpha helical region of PspA. Additionally, the families are further comprised of clades, wherein PspAs from strains which belong to a clade exhibit greater than 75% sequence homology in aligned sequences of the C-terminal region of the alpha helix of PspA. Vaccine compositions of the present invention preferably comprise a minimum of 4 and a maximum of 6 strains representing a single clade each, and the at least two PspAs are optionally serologically or broadly cross-reactive.

This application is a continuation of U.S. patent application Ser. No. 09/147,875, filed May 24, 1999 now U.S. Pat. No. 6,638,516, which is a continuation-in-part (“CIP”) of U.S. patent appilication Ser. No. 08/710,749, filed Sep. 20, 1996, now U.S. Pat. No. 5,955,089, and a U.S. National Application of PCT Application No. PCT/US97/16761, filed Sep. 22, 1997, all of which are incorporated herein by their entirety.

DESCRIPTION OF DEPOSITED BIOLOGICAL MATERIALS

The Streptococcus pneumoniae strain designated Rx1 has been deposited pursuant to, and in satisfaction of, the requirements of the Budapest Treaty on the International Recognition of The Deposit of Microorganisms for The Purposes of Patent Procedure, with the American Type Culture Collection (ATCC), now at 10801 University Boulevard, Manassas, Va. 20110-2209, under ATCC Accession No. 55834, on Oct. 3, 1996.

BACKGROUND OF THE INVENTION

Streptococcus pneumoniae is an important cause of otitis media, meningitis, bacteremia and pneumonia, and a leading cause of fatal infections in the elderly and persons with underlying medical conditions such as pulmonary disease, liver disease, alcoholism, sickle cell anemia, cerebrospinal fluid leaks, acquired immune deficiency syndrome (AIDS), and patients undergoing immunosuppressive therapy. It is also a leading cause of morbidity in young children. Pneumococcal infections cause approximately 40,000 deaths in the U.S. each year. The most severe pneumococcal infections involve invasive meningitis and bacteremia infections, of which there are 3,000 and 50,000 cases annually, respectively.

Despite the use of antibiotics and vaccines, the prevalence of pneumococcal infections has declined little over the last twenty-five years; the case-fatality rate for bacteremia is reported to be 15–20% in the general population, 30–40% in the elderly, and 36% in inner-city African Americans. Less severe forms of pneumococcal disease are pneumonia, of which there are 500,000 cases annually in the U.S., and otitis media in children, of which there are an estimated 7,000,000 of such cases each year are caused by pneumococcus. Strains of drug-resistant S. pneumoniae are becoming ever more common in the U.S. and worldwide. In some areas, as many as 30% of pneumococcal isolates are resistant to penicillin. The increase in antimicrobial resistant pneumococcus further emphasizes the need for preventing pneumococcal infections.

Pneumococcus asymptomatically colonizes the upper respiratory tract of normal individuals; disease often results from the spread of organisms from the nasopharynx to other tissues during opportunistic events. The incidence of carriage in humans varies with age and circumstances. Carrier rates in children are typically higher than those of adults. Studies have demonstrated that 38 to 60% of preschool children, 29 to 35% of grammar school children and 9 to 25% of junior high school children are carriers of pneumococcus. Among adults, the rate of carriage drops to 6% for those without children at home, and to 18 to 29% for those with children at home. It is not surprising that the higher rate of carriage in children than in adults parallels the incidence of pneumococcal disease in these populations.

An attractive goal for streptococcal vaccination is to reduce carriage in the vaccinated populations and subsequently reduce the incidence of pneumococcal disease. There is speculation that a reduction in pneumococcal carriage rates by vaccination could reduce the incidence of the disease in non-vaccinated individuals as well as vaccinated individuals. This “herd immunity” induced by vaccination against upper respiratory bacterial pathogens has been observed using the Haemophilus influenzae type b conjugate vaccines (Takala, A. K., et al., J. Infect. Dis. 1991; 164:982–986; Takala, A. K., et al., Pediatr. Infect. Dis. J., 1993; 12:593–599; Ward, J., et al., Vaccines, S. A. Plotkin and E. A. Mortimer, eds., 1994, pp. 337–386; Murphy, T. V., et al., J. Pediatr., 1993; 122; 517–523; and Mohle-Boetani, J. C., et al., Pediatr. Infect. Dis. J, 1993; 12:589–593).

It is generally accepted that immunity to Streptococcus pneumoniae can be mediated by specific antibodies against the polysaccharide capsule of the pneumococcus. However, neonates and young children fail to make adequate immune response against most capsular polysaccharide antigens and can have repeated infections involving the same capsular serotype. One approach to immunizing infants against a number of encapsulated bacteria is to conjugate the capsular polysaccharide antigens to protein to make them immunogenic. This approach has been successful, for example, with Haemophilus influenzae b (see U.S. Pat. No. 4,496,538 to Gordon and U.S. Pat. No. 4,673,574 to Anderson).

However, there are over ninety known capsular serotypes of S. pneumoniae, of which twenty-three account for about 95% of the disease. For a pneumococcal polysaccharide-protein conjugate to be successful, the capsular types responsible for most pneumococcal infections would have to be made adequately immunogenic. This approach may be difficult, because the twenty-three polysaccharides included in the presently-available vaccine are not all adequately immunogenic, even in adults.

Protection mediated by anti-capsular polysaccharide antibody responses are restricted to the polysaccharide type. Different polysaccharide types differentially facilitate virulence in humans and other species. Pneumococcal vaccines have been developed by combining 23 different capsular polysaccharides that are the prevalent types of human pneumococcal disease. These 23 polysaccharide types have been used in a licensed pneumococcal vaccine since 1983 (D. S. Fedson and M. Musher, Vaccines, S. A. Plotkin and J. E. A. Montimer, eds., 1994, pp. 517–564). The licensed 23-valent polysaccharide vaccine has a reported efficacy of approximately 60% in preventing is bacteremia caused by vaccine type pneumococci in healthy adults.

However, the efficacy of the vaccine has been controversial, and at times, the justification for the recommended use of the vaccine questioned. It has been speculated that the efficacy of this vaccine is negatively affected by having to combine 23 different antigens. Having a large number of antigens combined in a single formulation may negatively affect the antibody responses to individual types within this mixture because of antigenic competition. The efficacy is also affected by the fact that the 23 serotypes encompass all serological types associated with human infections and carriage.

An alternative approach for protecting children, and also the elderly, from pneumococcal infection would be to identify protein antigens that could elicit protective immune responses. Such proteins may serve as a vaccine by themselves, may be used in conjunction with successful polysaccharide-protein conjugates, or as carriers for polysaccharides.

McDaniel et al. (I), J. Exp. Med. 160:386–397, 1984, relates to the production of monoclonal antibodies that recognize cell surface polypeptide(s) on S. pneumoniae and protection of mice from infection with certain strains of encapsulated pneumococci by such antibodies.

This surface protein antigen has been termed “pneumococcal surface protein A”, or “PspA” for short.

McDaniel et al. (II), Microbial Pathogenesis 1:519–531, 1986, relates to studies on the characterization of the PspA. Considerable diversity in the PspA molecule in different strains was found, as were differences in the epitopes recognized by different antibodies.

McDaniel et al. (III), J. Exp. Med. 165:381–394, 1987, relates to immunization of X-linked immunodeficient (XID) mice with non-encapsulated pneumococci expressing PspA protects mice from subsequent fatal infection with pneumococci, but immunization with isogenic pneumococci which do not express PspA does not confer protection.

McDaniel et al. (IV), Infect. Immun., 59:222–228, 1991, relates to immunization of mice with a recombinant full length fragment of PspA that is able to elicit protection against pneumococcal strains of capsular types 6A and 3.

Crain et al, Infect.Immun., 56:3293–3299, 1990, relates to a rabbit antiserum that detects PspA in 100% (n=95) of clinical and laboratory isolates of strains of S. pneumoniae. When reacted with seven monoclonal antibodies to PspA, fifty-seven S. pneumoniae isolates exhibited thirty-one different patterns of reactivity.

U.S. Pat. No. 5,476,929, relates to vaccines comprising PspA and fragments thereof, methods for expressing DNA encoding PspA and fragments thereof, DNA encoding PspA and fragments thereof, the amino acid sequences of PspA and fragments thereof, compositions containing PspA and fragments thereof and methods of using such compositions.

PspA has been identified as a virulence factor and protective antigen. PspA is a cell surface molecule that is found on all clinical isolates, and the expression of PspA is required for the full virulence of pneumococci in mouse models (McDaniel et al., (III), J. Exp. Med. 165:381–394, 1987). The biological function of PspA has not been well defined, although a preliminary report suggests that it may inhibit complement activation (Alonso DeVelasco, E., et al., Microbiological Rev. 1995; 59:591–603).

The PspA protein type is independent of capsular type. It would seem that genetic mutation or exchange in the environment has allowed for the development of a large pool of strains which are highly diverse with respect to capsule, PspA, and possibly other molecules with variable structures. Variability of PspA's from different strains also is evident in their molecular weights, which range from 67 to 99 kD. The observed differences are stably inherited and are not the result of protein degradation.

Immunization with PspA in a lysate of a recombinant lgt11 clone, elicited protection against challenge with several S. pneumoniae strains representing different capsular and PspA types, as in McDaniel et al. (IV), Infect. Immun. 59:222–228, 1991. Although clones expressing PspA were constructed according to that paper, the product was insoluble and isolation from cell fragments following lysis was not possible.

Analysis of the nucleotide and amino acid sequences of the PspA molecule reveals three major regions. The first 288 amino acids at the amino terminal end of the protein are predicted to have a strong alpha helical structure. The adjacent region of 90 amino acids (289 to 369 of Rx1 PspA) has a high density of proline residues; based on similar regions in other prokaryotic proteins, this region is believed to traverse the bacterial cell wall. The remaining 196 amino acids at the carboxyl-terminal end of the molecule (370 to 588 of Rx1 PspA) have a repeated amino acid sequence that has been demonstrated to bind to phosphocholine and lipoteichoic acids. Based on this structure, the PspA molecule is thought to associate with the inner membrane and lipoteichoic acids via the repeated region in the middle of the carboxyl-terminal end of the protein. The proline region in the middle of the protein is thought to traverse the cell wall, placing the alpha helical region on the outer surface of the S. pneumoniae cells. This model is consistent with the demonstration that the alpha helical region, which extends from the surface of the cell, contains the protective epitopes (Yother, J. et al., J. Bacteriol. 1992; 174:601–609; Yother, J. et al., J. Bacteriol. 1994; 176:2976–2985; McDaniel, L. S. et al., Microbial Pathog. 1994; 17:323–337; and Ralph, B. A., et al., Ann. N.Y. Acad. Sci. 1994; 730: 361–363).

Serological analysis of PspA using a panel of seven monoclonal antibodies, indicated that, like capsular polysaccharides, the PspA molecules are highly diverse among pneumococcal strains. Based on these analyses, over 30 PspA protein serotypes were defined, and individual strains were assigned into groups, i.e., families (or serotypes) using a classification system based upon reactivity with the panel of monoclonal antibodies. Moreover, SDS-PAGE analysis indicated that, within a PspA serotype, further heterogeneity existed on the basis of the molecular size. This diversification further supports the assertion that PspA is a protective antigen in natural infections; the protective nature of anti-PspA responses has presumably applied selective pressure on pneumococcus to diversify this molecule. However, this diversification of the PspA molecule complicates the development of a PspA vaccine, and leads to the possibility that a PspA vaccine would have to contain many PspA strains, possibly making the vaccine impractical.

Briles et al., PCT 92/000857, used a pspA-specific probe to identify related proteins among different strains of S. pneumoniae. One such PspA-like polypeptide has been designated PspC. (Abstracts of the 97th Annual Meeting of the American Societies for Microbiology, May 1997). The gene encoding PspC hybridizes to a full-length pspA probe, demonstrating the close relatedness of the PspA and PspC proteins at the molecular level. Comparison of consensus sequences for the PspA clades with known pspC genes indicates that some of the PspC proteins can be classified within the defined PspA clades. In fact, sequence analysis of pspC genes from distinct isolates of S. pneumoniae reveals a greater than 85% homology at the amino acid level between the products of these pspC genes and those of pspA genes from representatives of Clade 2. Furthermore, PspC contains the same three major regions described hereinabove for PspA, namely an alpha helical N-terminal domain, a proline-rich region, and a choline binding C-terminal domain. Also, polyclonal antibodies raised against PspC cross-react with PspA proteins. Thus, for the purposes of the present invention, the term “PspA”, as it appears in the specifications and in the claims appended thereto, includes full-length and truncated forms of naturally-occurring, synthetic, semi-synthetic or recombinant forms of PspA of PspC.

In addition to the published literature specifically referred to above, the inventors, in conjunction with co-workers, have published further details concerning PspAs, as follows:

-   -   1. Abstracts of 89th Annual Meeting of the American Society for         Microbiology, p. 125, item D-257, May 1989;     -   2. Abstracts of 90th Annual Meeting of the American Society for         Microbiology, p. 98, item D-106, May 1990;     -   3. Abstracts of 3rd International ASM Conference on         Streptococcal Genetics, p. 11, item 12, June 1990;     -   4. Talkington et al, Infect. Immun. 59:1285–1289, 1991;     -   5. Yother et al (I), J.Bacteriol. 174:601–609, 1992; and     -   6. Yother et al (II), J. Bacteriol. 174:610–618, 1992.     -   7. McDaniel et al (V), Microbiol. Pathogenesis, 13:261–268,         1994.

Alternative vaccination strategies are desirable as such provide alternative routes to administration or alternative routes to generation of immune responses. It would be advantageous to provide an immunological composition or vaccination regimen which elicits protection against various diverse pneumococcal strains, without having to combine a large number of possibly competitive antigens within the same formulation.

The prior art fails to provide broadly efficacious pneumococcal vaccines. Surprisingly, the present inventions technique of clade and family groups within the Pneumococci solves this deficiency of prior art approaches by allowing a rational selection of representative PspAs from the various families of clades to produce broadly efficacious Pneumococcal vaccines, reagents and methods.

The present invention provides a vaccine composition comprising at least two PspAs from strains selected from at least two families. A family is defined by PspAs from strains having greater than or equal to 50% homology in aligned sequences of a C-terminal region of an alpha helix of PspA.

The invention provides vaccine compositions, wherein the families further comprise one or more clades. Glades are defined by PspAs having greater than 75% homology in the aligned sequences of the C-terminal region of the alpha helix of PspA.

Additionally, the present invention provides vaccine compositions wherein the C-terminal region of PspA contains epitope(s) of interest.

The present invention further provides vaccine compositions wherein a central domain comprising the C-terminal 100 amino acids of the alpha-helical region (192 to 290 of Rx1 PspA) contains epitope(s) capable of eliciting a protective response.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows a Pustell DNA matrix analysis of homology between the PspA genes of Rx1 and EF10197 strains.

FIG. 2 shows a Pustell protein matrix analysis of homology between the PspA proteins of Rx1 and EF10197 strains.

FIG. 3 shows the alignment of PspA protein amino acid sequences from the BG6692 strain (SEQ ID NO: 2), the BG8838 strain (SEQ ID NO: 3), the BG9739 strain (SEQ ID NO: 4), the DBL6A strain (SEQ ID NO: 5), the L81905 strain (SEQ ID NO: 6), the BG8743 strain (SEQ ID NO: 7), the DBL1 strain (SEQ ID NO: 8), and the AC94 strain (SEQ ID NO: 9) to the PspA clade 1 consensus sequence (SEQ ID NO: 1). FIG. 3 corresponds to the data presented in Table 3.

FIG. 4 shows the alignment of PspA protein amino acid sequences from the EF10197 strain (SEQ ID NO: 11), the Rx1 strain (SEQ ID NO: 12), the WU2 strain (SEQ ID NO: 13), the DBL5 strain (SEQ ID NO: 14), the EF6796 strain (SEQ ID NO: 15), the 0922134 strain (SEQ ID NO: 16), and the BG9163 strain (SEQ ID NO: 17) to the PspA clade 2 consensus sequence (SEQ ID NO: 10). FIG. 4 corresponds to the data presented in Table 4.

FIG. 5 shows the alignment of PspA protein amino acid sequences from the AC122 strain (SEQ ID NO: 19), the EF3296 strain (SEQ ID NO: 20), and the BG8090 strain (SEQ ID NO: 21) to the PspA clade 3 consensus sequence (SEQ ID NO: 18). FIG. 5 corresponds to the data presented in Table 5.

FIG. 6 shows the alignment of PspA protein amino acid sequences from the BG11703 strain (SEQ ID NO: 23), the BG7817 strain (SEQ ID NO: 24), the EF5668 strain (SEQ ID NO: 25), and the BG7561 strain (SEQ ID NO: 26) to the PspA clade 4 consensus sequence (SEQ ID NO: 22). FIG. 6 corresponds to the data presented in Table 6.

FIG. 7 shows the amino acid sequence of PspA from strain ATCC6303 (SEQ ID NO: 27), a representative strain of clade 5.

FIG. 8 shows the amino acid sequence of PspA from strain BG6380 (SEQ ID NO: 28), a representative strain of clade 6.

FIG. 9 shows the competitive inhibition of rabbit polyclonal anti-Rx1 by PA314, recombinant Rx1 containing amino acids 96 to 314.

FIG. 10 shows the inhibition of polyclonal rabbit anti-Rx1 antibodies by PARx1 and PAEF5668 antigens.

FIG. 11 shows the inhibition of polyclonal rabbit anti-Rx1 antibodies by PARx1 and PABG6380 antigens.

DETAILED DESCRIPTION

It has now been surprisingly found that, despite the assertions of the prior art regarding the apparent diversity of PspA from strains, the primary sequence of the alpha helix of PspA has two regions of relative conservation and a region of extensive diversity between PspAs from stains. The two regions of relative conservation are comprised of the first, N-terminal, 60 amino acids of the alpha helix, and the last, C-terminal, about 100 amino acids of the alpha helix, as shown in FIGS. 1 and 2, wherein the C-terminal end of the alpha helix contains cross-reactive and protective epitopes that are critical to the development of a broadly efficacious PspA vaccine. It has been found that any conservation in the first, N-terminal, 60 amino acids of the alpha helix is of little consequence in the cross-reactivity of the strain, and hence, is irrelevant to the development of a PspA vaccine.

A comparison of the amino acid sequences in the C-terminal region of the alpha helix of PspAs from 24 strains of S. pneumoniae has revealed that the PspA strains can be grouped into 6 clades with greater than 75% homology, and these clades can be grouped into 4 families with greater than 50% homology.

Accordingly, the present invention provides a method of strain selection of PspA, based upon the sequence homology of PspAs in the C-terminal region of the alpha helix.

A clade is defined herein as comprising PspAs which exhibit greater than 75% sequence homology in aligned sequences of the C-terminal region of the alpha helix, and family is defined herein as those clades which exhibit greater than or equal to 50% homology between member PspA sequences in aligned sequences of the C-terminal region of the alpha helix.

Further, it has been found that in addition to sequence homology, members of a clade exhibit cross-reactivity and cross-protection among one another, which may suggest a causal relationship between sequence homology and cross-reactivity. PspAs of strains within the same PspA clade exhibit reciprocal cross-protection from immunization and challenge experiments. It has not been heretofore recognized in the prior art that there may be such a causal relationship; in fact, families of PspA strains were defined solely on the basis of serological cross-reactivity and, based upon the prior art definition of families of PspA strains, it was believed that the extreme diversity of the PspA molecule would result in a futile attempt at strain selection. Moreover, the PspA typing system (Crain, et al., Infect. Immun. 59: 222–228, 1990) failed to provide relevant groupings of strains, and suggested an enormous diversity.

Hence, the present invention, in contrast to the teachings of the prior art, enables the selection of PspAs from strains in accordance with sequence homology and cross-reactivity, which facilitates the development of vaccine compositions comprising multiple PspAs.

The present invention contemplates vaccine compositions comprising two or more, preferably no more than 10, and more preferably a minimum of 4 and a maximum 6 strains of PspA representing a single clade each, and a pharmaceutically acceptable carrier or diluent. In a preferred embodiment, Rx1, a member of clade 2, is the preferred strain of clade 2 and/or family 1 which is optionally included in the vaccine composition of the present invention.

The aforementioned definition of a family structure to the C-terminal end of the alpha helix region enables the development of a broadly efficacious pneumococcal vaccine composition with a limited number of strains. Combining strains that represent some or all of the families for this cross-reactive and protective region should provide broad protection against pneumococcal disease. Not all clades may need to be represented because of cross-reactions between some clades within families or because of the epidemiology of these strains or clades in the population to be vaccinated. However, it is well within the scope of knowledge of the skilled artisan to determine those strains which should be included within a vaccine composition, without the burden of undue experimentation. Additionally, the selected PspAs and PspA-like polypeptides of the present invention further contain epitope(s) of interest which can elicit an immune response. An epitope of interest is that portion of an antigen or immunogen of interest which is capable of interacting with an antibody or T cell.

The present invention provides an immunogenic, immunological or vaccine composition containing pneumococcal strain(s) having an epitope of interest, and a pharmaceutically acceptable carrier or diluent. An immunological composition containing the PspAs having an epitope of interest, elicits an immunological response—local or systemic. The response can, but need not be, protective. An immunogenic composition containing the PspAs having an epitope of interest, likewise elicits a local or systemic immunological response which can, but need not be, protective. A vaccine composition elicits a local or systemic protective response. Accordingly, the terms “immunological composition” and “immunogenic composition” include a “vaccine composition” (as the two former terms can be protective compositions).

The invention therefore also provides a method of inducing an immunological response in a host mammal comprising administering to the host an immunogenic, immunological or vaccine composition comprising PspAs having an epitope of interest, and a pharmaceutically acceptable carrier or diluent. As to epitopes of interest, one skilled in the art can often identify epitopes or immunodominant regions of a peptide or polypeptide, and ergo, the coding DNA therefor from the knowledge of the amino acid and corresponding DNA sequences of the peptide or polypeptide, as well as from the nature of particular amino acids (e.g., size, charge, etc.) and the codon dictionary, without undue experimentation.

A general method for determining which portions of a protein to use in an immunological composition focuses on the size and sequence of the antigen of interest. “In general, large proteins, because they have more potential determinants are better antigens than small ones. The more foreign an antigen, that is the less similar to self configurations which induce tolerance, the more effective it is in provoking an immune response.” Ivan Roitt, Essential Immunology, 1988.

At a minimum, such a peptide must be at least 8 or 9 amino acids long. This is the minimum length that a peptide needs to be in order to stimulate a CD4+ T cell response (which recognizes virus infected cells or cancerous cells). A minimum peptide length of 13 to 25 amino acids is useful to stimulate CD8+ T cell response (which recognizes special antigen presenting cells which have engulfed the pathogen). See Kendrew, supra. However, as these are minimum lengths, these peptides are likely to generate an immunological response, i.e., an antibody or T cell response; but, for a protective response (as from a vaccine composition), a longer peptide is preferred.

With respect to the sequence, the DNA sequence encoding the immunogenic peptide preferably encodes at least regions of the peptide that generate an antibody response or a T cell response. One method to determine T and B cell epitopes involves epitope mapping. The protein of interest “is fragmented into overlapping peptides with proteolytic enzymes. The individual peptides are then tested for their ability to bind to an antibody elicited by the native protein or to induce T cell or B cell activation. This approach has been particularly useful in mapping T-cell epitopes since the T cell recognizes short linear peptides complexed with MHC molecules. The method is less effective for determining B-cell epitopes” since B cell epitopes are often not linear amino acid sequence but rather result from the tertiary structure of the folded three dimensional protein. Janis Kuby, Immunology, pp. 79–80 (1992).

In the case of PspA, the location of the major cross-reactive region at the C-terminal 100 amino acids of the alpha-helical region was carried out with recombinant peptides of 100 or more amino acids in length (McDaniel et al., Micro. Pathog. 17:323–337, 1994).

Another method for determining an epitope of interest is to choose the regions of the protein that are hydrophilic. Hydrophilic residues are often on the surface of the protein and therefore often the regions of the protein which are accessible to the antibody. Janis Kuby, Immunology, p. 81 (1992).

Yet another method for determining an epitope of interest is to perform an X-ray crystallographic analysis of the antigen (full length)-antibody complex. Janis Kuby, Immunology, p. 80 (1992).

An immune response is generated, in general, as follows: T cells recognize proteins only when the protein has been cleaved into smaller peptides, which are then presented to the T cells in a complex called the major histocompatability complex (“MHC”) located on another cell's surface. There are two classes of MHC complexes—class I and class II, and each class is made up of many different alleles. Different patients have different types of MHC complex alleles; they are said to have a different “HLA type”.

Class I MHC complexes are found on virtually every cell and present peptides from proteins produced inside the cell. Thus, Class I MHC complexes are useful for killing cells which have been infected by viruses or which have become cancerous and as the result of expression of an oncogene. T cells which have a protein called CD4 on their surface bind to the MHC class I cells and secrete lymphokines. The lymphokines stimulate a response; cells arrive and kill the virus-infected cell. Class II MHC complexes are found only on antigen-presenting cells and are used to present peptides from circulating pathogens which have been endocytosed by the antigen-presenting cells. T cells which have a protein called CD8 bind to the MHC class II cells and kill the cell by exocytosis of lytic granules.

Thus, another method for identifying epitopes of interest is to identify those regions of the protein which can generate a T cell response. In order to generate a T cell response, a peptide which comprises a putative epitope should be presented in the context of a MHC complex. Those skilled in the art can identify from the protein sequence of the antigen of interest potential human lymphocyte antigen (“HLA”) anchor binding motifs. HLA anchor binding motifs are peptide sequences which are known to be likely to bind to the MHC molecule. The peptide preferably contains appropriate anchor motifs for binding to the MHC molecules, and should bind with high enough affinity to generate an immune response. Other factors which can be considered are: the HLA type of the patient (vertebrate, animal or human) expected to be immunized, the sequence of the protein, the presence of appropriate anchor motifs and the occurrence of the peptide sequence in other vital cells.

Some guidelines in determining whether a protein contains epitopes of interest capable of stimulating a T cell response, include: Peptide length—the peptide should be at least 8 or 9 amino acids long to fit into the MHC class I complex and at least 13–25 amino acids long to fit into a class II MHC complex. This length is a minimum for the peptide to bind to the MHC complex. It is preferred for the peptides to be longer than these lengths because cells may cut the expressed peptides. The peptide should contain an appropriate anchor motif which will enable it to bind to the various class I or class II molecules with high enough specificity to generate an immune response (See Bocchia, M. et al, “Specific Binding of Leukemia Oncogene Fusion Protein Peptides to HLA Class I Molecules,” Blood 85:2680–2684; Englehard, V H, “Structure of Peptides Associated with Class I and Class II MHC Molecules,” Ann. Rev. Immunol. 12:181 (1994)). This can be done, without undue experimentation, by comparing the sequence of the protein of interest with published structures of peptides associated with the MHC molecules. Protein epitopes recognized by T cell receptors are peptides generated by enzymatic degradation of the protein molecule and are presented on the cell surface in association with class I or class II MHC molecules.

Further, the skilled artisan can ascertain an epitope of interest by comparing the protein sequence with sequences listed in the protein data base. Regions of the protein which share little or no homology are better choices for being an epitope of that protein and are therefore useful in a vaccine or immunological composition. Regions which share great homology with widely found sequences present in vital cells should be avoided.

Even further, another method is simply to generate or express portions of a protein of interest, generate monoclonal antibodies to those portions of the protein of interest, and then ascertain whether those antibodies inhibit growth in vitro of the pathogen from which the protein was derived. The skilled artisan can use the other guidelines set forth in this disclosure and in the art for generating or expressing portions of a protein of interest for analysis as to whether antibodies thereto inhibit growth in vitro. For example, the skilled artisan can generate portions of a protein of interest by: selecting 8 to 9 or 13 to 25 amino acid length portions of the protein, selecting hydrophilic regions, selecting portions shown to bind from X-ray data of the antigen (full length)-antibody complex, selecting regions which differ in sequence from other proteins, selecting potential LA anchor binding motifs, or any combination of these methods or other methods known in the art.

Epitopes recognized by antibodies are expressed on the surface of a protein. To determine the regions of a protein most likely to stimulate an antibody response one skilled in the art can preferably perform an epitope map, using the general methods described above, or other mapping methods known in the art.

As can be seen from the foregoing, without undue experimentation, from this disclosure and the knowledge in the art, the skilled artisan can ascertain the amino acid and corresponding DNA sequence of an epitope of interest for obtaining a T cell, B cell and/or antibody response. In addition, reference is made to Defter et al., U.S. Pat. No. 5,019,384, issued May 28, 1991, and the documents it cites, incorporated herein by reference (Note especially the “Relevant Literature” section of this patent, and column 13 of this patent which discloses that: “A large number of epitopes have been defined for a wide variety of organisms of interest. Of particular interest are those epitopes to which neutralizing antibodies are directed. Disclosures of such epitopes are in many of the references cited in the Relevant Literature section.”)

Further, the invention demonstrates that more than one serologically complementary PspA molecule can be in an antigenic, immunological or vaccine composition, so as to elicit better response, e.g., protection, for instance, against a variety of strains of pneumococci; and, the invention provides a system of selecting PspAs for a multivalent composition which includes cross-protection evaluation so as to provide a maximally efficacious composition. The determination of the amount of antigen, e.g., PspA or truncated portion thereof and optional adjuvant in the inventive compositions and the preparation of those compositions can be in accordance with standard techniques well known to those skilled in the pharmaceutical or veterinary arts. In particular, the amount of antigen and adjuvant in the inventive compositions and the dosages administered are determined by techniques well known to those skilled in the medical or veterinary arts taking into consideration such factors as the particular antigen, the adjuvant (if present), the age, sex, weight, species and condition of the particular animal or patient, and the route of administration. For instance, dosages of particular PspA antigens for suitable hosts in which an immunological response is desired, can be readily ascertained by those skilled in the art from this disclosure, as is the amount of any adjuvant typically administered therewith. Thus, the skilled artisan can readily determine the amount of antigen and optional adjuvant in compositions and to be administered in methods of the invention. Typically, an adjuvant is commonly used as 0.001 to 50 wt % solution in phosphate buffered saline, and the antigen is present on the order of micrograms to milligrams, such as about 0.0001 to about 5 wt %, preferably about 0.0001 to about 1 wt %, most preferably about 0.0001 to about 0.05 wt % (see, e.g., Examples below or in applications cited herein). Typically, however, the antigen is present in an amount on the order of micrograms to milligrams, or, about 0.001 to about 20 wt %, preferably about 0.01 to about 10 wt %, and most preferably about 0.05 to about 5 wt %.

Of course, for any composition to be administered to an animal or human, including the components thereof, and for any particular method of administration, it is preferred to determine therefor: toxicity, such as by determining the lethal dose (LD) and LD₅₀ in a suitable animal model e.g., rodent such as mouse; and, the dosage of the composition(s), concentration of components therein and timing of administering the composition(s), which elicit a suitable immunological response, such as by titrations of sera and analysis thereof for antibodies or antigens, e.g., by ELISA and/or RFFIT analysis. Such determinations do not require undue experimentation from the knowledge of the skilled artisan, this disclosure and the documents cited herein. And, the time for sequential administrations can be ascertained without undue experimentation.

Examples of compositions of the invention include liquid preparations for orifice, e.g., oral, nasal, anal, vaginal, peroral, intragastric, mucosal (e.g., perlingual, alveolar, gingival, olfactory or respiratory mucosa) etc., administration such as suspensions, syrups or elixirs; and, preparations for parenteral, subcutaneous, intradermal, intramuscular or intravenous administration (e.g., injectable administration), such as sterile suspensions or emulsions. Such compositions may be in admixture with a suitable carrier, diluent, or excipient such as sterile water, physiological saline, glucose or the like. The compositions can also be lyophilized. The compositions can contain auxiliary substances such as wetting or emulsifying agents, pH buffering agents, gelling or viscosity enhancing additives, preservatives, flavoring agents, colors, and the like, depending upon the route of administration and the preparation desired. Standard texts, such as “REMINGTON'S PHARMACEUTICAL SCIENCE”, 17th edition, 1985, incorporated herein by reference, may be consulted to prepare suitable preparations, without undue experimentation.

Compositions of the invention are conveniently provided as liquid preparations, e.g., isotonic aqueous solutions, suspensions, emulsions or viscous compositions which may be buffered to a selected pH. If digestive tract absorption is preferred, compositions of the invention can be in the “solid” form of pills, tablets, capsules, caplets and the like, including “solid” preparations which are time-released or which have a liquid filling, e.g. gelatin covered liquid, whereby the gelatin is dissolved in the stomach for delivery to the gut. If nasal or respiratory (mucosal) administration is desired, compositions may be in a form and dispensed by a squeeze spray dispenser, pump dispenser or aerosol dispenser. Aerosols are usually under pressure by means of a hydrocarbon. Pump dispensers can preferably dispense a metered dose or a dose having a particular particle size.

Compositions of the invention can contain pharmaceutically acceptable flavors and/or colors for rendering them more appealing, especially if they are administered orally. The viscous compositions may be in the form of gels, lotions, ointments, creams and the like and will typically contain a sufficient amount of a thickening agent so that the viscosity is from about 2500 to 6500 cps, although more viscous compositions, even up to 10,000 cps may be employed. Viscous compositions have a viscosity preferably of 2500 to 5000 cps, since above that range they become more difficult to administer. However, above that range, the compositions can approach solid or gelatin forms which are then easily administered as a swallowed pill for oral ingestion.

Liquid preparations are normally easier to prepare than gels, other viscous compositions, and solid compositions. Additionally, liquid compositions are somewhat more convenient to administer, especially by injection or orally, to animals, children, particularly small children, and others who may have difficulty swallowing a pill, tablet, capsule or the like, or in multi-dose situations. Viscous compositions, on the other hand, can be formulated within the appropriate viscosity range to provide longer contact periods with mucosa, such as the lining of the stomach or nasal mucosa.

Obviously, the choice of suitable carriers and other additives will depend on the exact route of administration and the nature of the particular dosage form, e.g., liquid dosage form (e.g., whether the composition is to be formulated into a solution, a suspension, gel or another liquid form), or solid dosage form (e.g., whether the composition is to be formulated into a pill, tablet, capsule, caplet, time release form or liquid-filled form).

Solutions, suspensions and gels, normally contain a major amount of water (preferably purified water) in addition to the antigen, and optional adjuvant. Minor amounts of other ingredients such as pH adjusters (e.g., a base such as NaOH), emulsifiers or dispersing agents, buffering agents, preservatives, wetting agents, jelling agents, (e.g., methylcellulose), colors and/or flavors may also be present. The compositions can be isotonic, i.e., it can have the same osmotic pressure as blood and lacrimal fluid.

The desired isotonicity of the compositions of this invention may be accomplished using sodium chloride, or other pharmaceutically acceptable agents such as dextrose, boric acid, sodium tartrate, propylene glycol or other inorganic or organic solutes. Sodium chloride is preferred particularly for buffers containing sodium ions.

Viscosity of the compositions may be maintained at the selected level using a pharmaceutically acceptable thickening agent. Methylcellulose is preferred because it is readily and economically available and is easy to work with. Other suitable thickening agents include, for example, xanthan gum, carboxymethyl cellulose, hydroxypropyl cellulose, carbomer, and the like. The preferred concentration of the thickener will depend upon the agent selected. The important point is to use an amount which will achieve the selected viscosity. Viscous compositions are normally prepared from solutions by the addition of such thickening agents.

A pharmaceutically acceptable preservative can be employed to increase the shelf-life of the compositions. Benzyl alcohol may be suitable, although a variety of preservatives including, for example, parabens, thimerosal, chlorobutanol, or benzalkonium chloride may also be employed. A suitable concentration of the preservative will be from 0.02% to 2% based on the total weight although there may be appreciable variation depending upon the agent selected.

Those skilled in the art will recognize that the components of the compositions must be selected to be chemically inert with respect to the PspA antigen and optional adjuvant. This will present no problem to those skilled in chemical and pharmaceutical principles, or problems can be readily avoided by reference to standard texts or by simple experiments (not involving undue experimentation), from this disclosure and the documents cited herein.

The immunologically effective compositions of this invention are prepared by mixing the ingredients following generally accepted procedures. For example the selected components may be simply mixed in a blender, or other standard device to produce a concentrated mixture which may then be adjusted to the final concentration and viscosity by the addition of water or thickening agent and possibly a buffer to control pH or an additional solute to control tonicity. Generally the pH may be from about 3 to 7.5. Compositions can be administered in dosages and by techniques well known to those skilled in the medical and veterinary arts taking into consideration such factors as the age, sex, weight, and condition of the particular patient or animal, and the composition form used for administration (e.g., solid vs. liquid). Dosages for humans or other animals can be determined without undue experimentation by the skilled artisan from this disclosure, the documents cited herein and the Examples below (e.g., from the Examples involving mice).

Suitable regimes for initial administration and booster doses or for sequential administrations also are variable, may include an initial administration followed by subsequent administrations; but nonetheless, may be ascertained by the skilled artisan from this disclosure, the documents cited herein and the Examples below.

The following Examples are provided for illustration and are not to be considered a limitation of the invention.

EXAMPLES Example 1

Identification of Sequence Homologies Between PspAs

Despite the described diversity of PspA strains, the nucleotide and amino acids sequences of the PspA molecule has been evaluated with respect to whether any region(s) of conservation have been maintained which could be of utility to vaccine development. The comparison of the nucleotide and amino acid sequences from multiple strains of PspA revealed that the primary sequence of the alpha helix has two regions of relative conservation and a region of extensive diversity between strains. The two regions of diversity are comprised of the first, N-terminal, 60 amino acids of the alpha helix, and the last, C-terminal, 100 amino acids of the alpha helix, as shown in FIGS. 1 and 2.

FIG. 1 shows the nucleotide sequences of the alpha helix and proline regions of the pspA genes from Rx1 and EF10197, both members of the same family or clade, as compared to each other for regions of homology. This comparison was made using a Pustell DNA matrix analysis within the MacVector version 5.0.2 software, using a window of 30 nucleotides, a minimum percentage of homology of 70%, a hash value of 6, and a jump value of 1. Points or lines in the graph indicate regions of homology between the two genes that meet the aforementioned criteria. The results demonstrate homology in the portions of the genes encoding the N-terminal and C-terminal ends of the alpha helix region, as well as the proline region.

FIG. 2 shows the amino acid sequence comparison of the alpha helix and proline regions of the PspA proteins from Rx1 and EF10197, both members of the same family or clade, as compared to each other for regions of homology. This comparison was made using a Pustell protein matrix analysis within the MacVector version 5.0.2 software. The analysis was done using a window of 8 amino acids, a minimum percentage homology of 70%, a hash value of 2, and the pam250 scoring matrix. Points or lines in the graph indicate regions of homology between the two proteins. The results demonstrate homology in the N-terminal and the C-terminal ends of the alpha helix region, as well as in the proline region.

The conserved region at the C-terminal end of the alpha helix region correlated with a region demonstrated to contain protective epitopes that were conserved between two strains.

Reasoning that the C-terminal region of the alpha helix region was critical to vaccine development, the heterogeneity and family structure of amino acid sequences in this region was examined. The comparison of the amino acid sequences in this region between 26 strains of PspA revealed that the PspA strains could be grouped into 6 clades with greater than 75% homology. These clades could be grouped into 4 families with greater than 50% homology. These data are shown in Tables 1 to 6, and FIGS. 3 to 8.

TABLE 1 Family/Clade List % AMINO HOMOL- ACID OGY HOMOLOGY WITHIN TO CLADE FAMILY FAMILY CLADE STRAIN CONSENSUS Family 1 >50% Clade 1 BG9739 (SEQ ID 96 (SEQ ID NO:4) NO:1) DBL6A (SEQ ID 98 NO:5) L81905 (SEQ ID 94 NO:6) BG8743 (SEQ ID 87 NO:7) AC94 (SEQ ID 88 NO:9) BG6692 (SEQ ID 96 NO:2) BG8838 (SEQ ID 95 NO:3) DBL1 (SEQ ID 88 NO:8) Clade 2 EF10197 (SEQ 89 (SEQ ID ID NO:11) NO:10) RX1 (SEQ ID 92 NO:12) WU2 (SEQ ID 87 NO:13) 0922134 (SEQ ID 99 NO:16) DBL5 (SEQ ID 92 NO:14) BG9163 (SEQ ID 79 NO:17) EF6796 (SEQ ID 91 NO:15) Family 2 >50% Clade 3 EF3296 (SEQ ID 97 (SEQ ID NO:20) NO:18) AC122 (SEQ ID 96 NO:19) BG8090 (SEQ ID 96 NO:21) Family 3 >50% Clade 4 EF5668 (SEQ ID 92 (SEQ ID NO:25) NO:22) BG7817 (SEQ ID 96 NO:24) BG7561 (SEQ ID 89 NO:26) BG11703 (SEQ 100 ID NO:23) Clade 5 ATCC6303 (SEQ 100 ID NO:27) Family 4 >50% Clade 6 BG6380 (SEQ ID 100 NO:28)

TABLE 2A Homology Between Clades - Matrix of Amino Acid Similarity Estimates Between Clades Clade 1 Clade 2 Clade 3 Clade 4 Clade 5 Clade 6 Clade 1 >75% Clade 2 >50% >75% Clade 3 <25% <20% >75% Clade 4 <20% >30% >30% >75% Clade 5 <20% <20% >30% >50% >75% Clade 6 <10% <20% <10% <20% <20% >75%

TABLE 2B AA % sequence identities to PspA Clade Consensus % of AA that differ Strain Name from the Clade % AA identity to Clade (Capsular Type) Consensus Clade Consensus Clade 1 BG9739 (4) 4 96 DBL6A (6A) 2 98 L81905 (4) 6 94 BG8743 (23) 13 87 AC94 (9) 12 88 BG6692 (33) 4 96 BG8838 (6) 5 95 DBL1 (6B) 12 88 Clade 2 EF10197 (3) 10 89 RX1 (2) 8 92 WU2 (3) 13 87 0922134 (23) 1 99 DBL5 (5) 8 92 BG9163 (6B) 21 79 EF6796 (6A) 9 91 Clade 3 EF3296 (4) 1 97 AC122 (9) 2 96 BG8090 (19) 4 96 Clade 4 EF5668 (4) 9 92 BG7817 (7) 4 96 BG7561 (15) 12 89 BG11703 (N.D) 0 100 Clade 5 ATCC6303 (3) 0 100 Clade 6 BG6380 (37) 0 100 N.D. = not determined

TABLE 3 Sequence identities to PspA Clade 1 Consensus # OF AA THAT DIFFER FROM % AA IDENTITY THE CLADE TO CLADE CLADE STRAIN NAME CONSENSUS CONSENSUS Clade 1 BG9739 4 96 DBL6A 2 98 L81905 6 94 BG8743 13 87 AC94 12 88 BG6692 4 96 BG8838 5 95 DBL1 12 88

TABLE 4 Sequence identities to PspA Clade 2 consensus # OF AA THAT STRAIN DIFFER FROM THE % AA IDENTITY TO CLADE NAME CLADE CONSENSUS CLADE CONSENSUS Clade 2 EF10197 10 89 RX1 8 92 WU2 13 87 0922134 1 99 DBL5 8 92 BG9163 21 79 EF6796 9 91 RCT123 3 97 RCT129 1 99 RCT135 0 100 LXS200 0 100

TABLE 5 Sequence identities to PspA Clade 3 Consensus # OF AA THAT STRAIN DIFFER FROM THE % AA IDENTITY TO CLADE NAME CLAD CONSENSUS CLADE CONSENSUS Clade 3 EF3296 1 97 AC122 2 96 BG8090 4 96

TABLE 6 Sequence identities to PspA Clade 4 Consensus # OF AA THAT STRAIN DIFFER FROM THE % AA IDENTITY TO CLADE NAME CLAD CONSENSUS CLADE CONSENSUS Clade 4 EF5668 9 92 BG7817 4 96 BG7561 12 89 BG11703 0 100

The immnunological relevance of these families was demonstrated by serological analysis of S. pneumoniae strains with a large number of monoclonal antibodies made to several different PspAs. As shown in Table 7, the pattern of reactions with strains in clades 3, 4, 5 and 6 of monoclonal antibodies generally correlated with the defined clade by sequence.

TABLE 7 Ab Reactions Clades 3–6 Anti-PspA Monoclonal Antibodies Made to EF3296(P32) Made to EF5668(P56) STRAIN CLADE* 263D12 263F6 264A4 264A11 265E6 270B6 263B7 351G12 EF3296 3 X X X X X X X BG7140 X X X X X PMsv1281 X X X X X X VH1193 X X X X X X X EF5668 4 X BG7817 4 X BG7561 4 X BG11703 4 X BG7736 X BG7813 X BG7915 X BG10717-/ X 30 ATCC6– 5 X 306 BG7619 X BG7941 X BG13075-/ X 30 BG6380 6 X indicates a positive reaction *clade was determined by amino acid sequences

Example 2

Competitive Inhibition of Anti-Rx1 Polyclonal Antibodies with the PspA Antigens of Different Strains

Competitive inhibition of anti-PARx1 binding to PARx1 antigen was 15 analyzed using a BIAcore® sensory chip, coated with PARx1 antigen. The results are shown in FIG. 9. Rabbit polyclonal anti-PARx1 (1200 ng/ml) was allowed to react to the chip either alone, or in the presence of increasing concentration of PARx1 antigen (indicated by + in FIG. 9) or PA314 PspA antigen (indicated by squares in FIG. 9); the PA314 PspA antigen contains amino acids 96 to 314 of Rx1. The concentration of uninhibited antibody able to bind to the PARx1 antigen on the sensory chip surface was measured using mass transport measurements on the BIAcore® instrument. The mouse monoclonal IgG anti-PspA antibody, P81–122F10.A11 was used as a standard for these measurements.

The results of these experiments indicated that the N-terminal conserved region does not contain antigenic epitopes for the PspA response, and that the conserved region at the C-terminal end of the alpha helix contains cross-reactive and protective epitopes that are critical to the development of a broadly efficacious PspA vaccine. Further, FIG. 9 demonstrates the lack of relevance of the first 60 amino acids of the N-terminal region of the alpha helix, as the PA314 PspA antigen used in the competition assays above contains amino acids 96 to 314 of Rx1.

FIG. 10 shows the inhibition of PARx1 and PAEF5668 antigens. A BIAcore® sensory chip was coated with PARx1 antigen and rabbit polyclonal anti-PARx1 (7 mM) was allowed to react to the chip either alone, or in the presence of increasing concentration of PARx1 antigen (represented by squares in FIG. 10) or PAEF5668 antigen (represented by circles in FIG. 10). The concentration (mM) of these competitive antigens is shown on the X axis on a logarithmic scale, while the concentration (mM) of uninhibited polyclonal antibody able to bind to the PARx1 antigen on the sensory chip was measured using mass transport measurements on the BIAcore® instrument, and is shown on the Y axis in FIG. 10.

As expected, the concentration of active, non-competitively inhibited polyclonal anti-PARx1 decreased as the concentrations of competitive inhibitor increased. PARx1 antigen completely inhibited the polyclonal antibodies at sufficient concentrations of antigens in excess. The PAEF5668 antigen has a maximal inhibition of 8.4%. The mouse monoclonal IgG anti-PspA antibody, P81–122F10. A11 was used as a standard for calculating the concentrations of active polyclonal antibody in this assay.

The results of the inhibition study by PARx1 and PABG6380 antigens is to shown in FIG. 11. A BIAcore® sensory chip was coated with PARx1 antigen and rabbit polyclonal anti-PARx1(7 mM) was allowed to react to the chip either alone, or in the presence of increasing concentration of PARx1 antigen (represented by squares in FIG. 11), or PABG6380 antigens (represented by X's in FIG. 11). The concentration (mM) of these competitive antigens is shown on the X axis on a logarithmic scale, while the concentration (mM) of uninhibited polyclonal antibody able to bind to the PARx1 antigen on the sensory chip was measured using mass transport measurements on the BIAcore® instrument, and is shown on the Y axis in FIG. 11.

As expected, the concentration of active, non-competitively inhibited polyclonal anti-PARx1 decreased as the concentration of competitive inhibitor increased. PARx1 antigen completely inhibited the polyclonal antibodies at sufficient concentrations of antigen in excess. The PABG6380 antigen did not significantly inhibit the polyclonal antibody reaction. The mouse monoclonal IgG anti-PspA antibody P81–122F10.A11 was used as a standard for calculating the concentrations of active polyclonal antibody in the assay.

Further, Table 8 shows the results of inhibition studies of polyclonal rabbit anti-Rx1 antibodies with representative strains of selective clades. As shown in the Table, anti-Rx1 antibodies inhibit clade 2 effectively, but the inhibition of PspAs in clades which differ from the specificity of the antibody itself is less effective.

TABLE 8 Inhibition of Polyclonal Rabbit anti-Rx1 Antibodies (Inhibition of Anti-Clade 2 Antibody Reactivity) Clade 1 2 2 2 4 6 — Strain BG9739 RX1 R36A WU2 EF5668 BG6380 JY1119* Antigen BG9739/n PARx1 R36A/n WU2/n PAEF5668 PABG6380 JY1119/n Name Antigen native recom.** native native recom.** recom.** native Type % 35.4 100.0 100.0 91.4 8.4 0.0 0.0 Inhibition *JY1119 is an engineered PspA loss mutant and is used in this assay as a negative control **recom. = recombinant

Example 3

Competitive Inhibition of Clade Specific Anti-PspA Polyclonal Antibodies with PspA Antigens from Different Clades

Rabbit polyclonal antiserum was raised against recombinantly expressed PspA antigens from representatives of the six clades. BG9739 was chosen as the representative of clade 1, Rx1 was the representative of clade 2, EF3296 was the representative of clade 3, EF5668 was the representative of clade 4, ATCC 6303 was the representative of clade 5 and BG6380 was the representative of clade 6.

Recombinant PspA antigens from each of the clades were each covalently linked to individual BIAcore sensory chips. Next, clade-specific polyclonal anti-PspA antibodies were allowed to react with each chip, either alone or in the presence of increasing concentration of each recombinant PspA antigen. The active concentration of anti-PspA antibodies that could bind to the PspA on the chip were determined using mass transport measurement. By comparing concentrations of the active antibody in uninhibited reactions and in reactions inhibited by the addition of soluble PspA strains was determined. These results are illustrated as estimated cross-reactivities in Table 9.

Cross-reactivity analyses were also performed using recombinant PspA antigens to coat BIAcore chips and the clade-specific polyclonal antisera described above, inhibited with native PspA antigens from representative clades. The results of the estimated cross-reactivities are shown in Table 10, and compare favorably to the results obtained with the results shown in Table 9. In each case, representatives of the same clade demonstrate the greatest cross-reactivity. Representatives of different clades within the same family demonstrate moderate cross-reactivity, and representatives of different families show the least cross-reactivity.

TABLE 9 Cross-Reacting PspA Antigens Family 1 2 3 4 Clade 1 2 3 4 5 6 Strain BG9739 Rx1 EF3296 EF5668 ATC 6303 BG6380 Rabbit 1 1 BG9739 100 23 0 0 0 1 Anti-PspA 2 Rx1 34 100 0 5 0 3 Strain 2 3 EF3296 0 0 100 0 0 2 3 4 EF5668 4 5 10 100 67 1 5 ATCC 6303 0 0 7 86 100 0 4 6 BG6380 0 0 4 0 0 100

Example 4

Serotype Analysis of S. pneumoniae Strains by ELISA

Rabbit polyclonal antiserum was raised against recombinantly expressed PspA antigens from representatives of the six clades. BG739 was chosen as the representative of clade 1, Rx1 was the representative of clade 2, EF3296 was the representative of clade 3, EF5668 waste representative of clade 4, ATCC 6303 was the representative of clade 5 and BG6380 waste representative of clade 6.

Each of the antisera were first normalized to contain roughly equivalent specific activities. Then, sequential 1.5 fold dilutions of the antisera were reacted with ELISA plates coated with cetavalon lysates of representatives of each clade. As a negative control, the pspA gene of a S. pneumoniae strain was “knocked out”, i.e., rendered inactive by a recombination event, and cetavalon lysates of this knock out strain were used to coat ELISA plate wells. Next, each well was incubated with goat anti-rabbit IgG-alkaline phosphatase conjugates (Kierkegaard and Perry, Gaithersburg, Md.) and washed, then p-Nitrophenyl Phosphate (Sigma Diagnostics, St. Louis) was added. Results of the calorimetric reactions were read at 405 nm.

Mixtures of antisera were prepared, combining equal specific activities of anti-Rx1, EF3296 and EF5668 in one cocktail, and anti-Rx1, EF3296, EF5668 and B06380 in a second cocktail. These cocktails contained antibodies which reacted with clades 2, 3 and 4 or 2, 3, 4 and 6 and were used to approximate the ability of various vaccine combinations to confer broad immunity. Mixtures of these antibodies reacted well with each of the S. pneumoniae strains tested, demonstrating that combinations of vaccines based on the clade definitions of the present invention should confer immunity against a broad range of S. pneumoniae isolates.

Polyclonal antibodies to PspAs from individual clades demonstrated little cross-reactivity with representatives of other families. Significant cross-reactivity was observed between strains of clades 1 and 2 and between strains of clades 4 and 5. This observation is consistent with the grouping of these clades into families 1 and 3, respectively. Each strain could be serotyped and placed within a defined family or clade of PspA based on reactivity with polyclonal anti-PspA.

A total of 437 S. pneumoniae strains from the United States and Europe were evaluated by the polyclonal anti-PSA ELISA method. The results of this analysis are shown in Table 11.

TABLE 10 Percentage Cross Reactivity With Native PspA Antigens Cross-Reacting PspA Antigens of Family/Clade Family 1 2 3 4 Clade 1 2 3 4 5 6 Rabbit 1 1 >91–86   33–16 3–0 24–4  0 8 Anti-PspA 2 52–25 >85–50   3–0 12–8  4 3 Clade 2 3 0 2–0 >95–33   8–3 0 0 3 4 3–0 15–9  22–9  100–70  72 3 5 13–3  6–0 11–0  81–48 100 10 4 6 24–9  24–5  15–12 30–20 5 >80

TABLE 11 Source of % of Strains of that Clade (# of Strains) Total # of Strains Location 1 2 3 4 5 6 0 Strains CDC U.S.A. 9.2 (28) 31.4 (96) 25.8 (79) 26.1 (80) 2.3 (7)  3.9 (12) 1.3 (4) 306 PMC ? 7.1 (1) 57.1 (8) 14.3 (92)   0 (0)   0 (0) 14.3 (2) 7.1 (1) 14 UAB U.S.A., 9.4 (11) 47.0 (55) 14.5 (17) 18.8 (22) 4.3 (5)  3.4 (4) 1.7 (2) 117 Europe

Approximately 36% of all strains examined were serotyped as clade 2, 22% as clade 3 and 23% as clade 4. A vaccine comprised of PspAs from these three clades alone would cover greater than 80% of the S. pneumoniae strains examined (Table 11). Of the 437 strains examined, 98.4% of these strains could be serotyped into one of the six clades, again demonstrating the potential for a finite number of vaccine components, based on clade-specific PspAs, to confer broad immunity against infection caused by S. pneumoniae (Table 11). In fact, based on the high degree of cross-reactivity within families, a vaccine composition comprised of a single representative member of each family should confer such immunity.

Having thus described in detail certain preferred embodiments of the present invention, it is to be understood that the invention defined by the appended claims is not to be limited by particular details set forth in the above description, as many apparent variations thereof are possible without departing from the spirit or scope thereof.

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1. A vaccine or immunogenic composition comprising at least an isolated PspA and an isolated immunogenic fragment of PspA from S. pneumoniae strains from at least two PspA families, wherein the isolated PspA is from one PspA family and the isolated immunogenic fragment of PspA is from another PspA family and the at least two families comprise one or more clades selected from the group consisting of clade 1, clade 2, clade 3, clade 4, clade 5, and clade
 6. 2. The vaccine or immunogenic composition of claim 1, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from clade
 1. 3. The vaccine or immunogenic composition of claim 2, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA having an amino acid sequence of SEQ ID NO:
 1. 4. The vaccine or immunogenic composition of claim 2, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain BG6692 having an amino acid sequence of SEQ ID NO:
 2. 5. The vaccine or immunogenic composition of claim 2, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain BG8838 having an amino acid sequence of SEQ ID NO:
 3. 6. The vaccine or immunogenic composition of claim 2, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain BG9739 having an amino acid sequence of SEQ ID NO:
 4. 7. The vaccine or immunogenic composition of claim 2, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain DBL6A having an amino acid sequence of SEQ ID NO:
 5. 8. The vaccine or immunogenic composition of claim 2, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain L81905 having an amino acid sequence of SEQ ID NO:
 6. 9. The vaccine or immunogenic composition of claim 2, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain BG8743 having an amino acid sequence of SEQ ID NO:
 7. 10. The vaccine or immunogenic composition of claim 2, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain DBL1 having an amino acid sequence of SEQ ID NO:
 8. 11. The vaccine or immunogenic composition of claim 2, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain AC94 having an amino acid sequence of SEQ ID NO:
 9. 12. The vaccine or immunogenic composition of claim 1, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from clade
 2. 13. The vaccine or immunogenic composition of claim 12, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA having an amino acid sequence of SEQ ID NO:
 10. 14. The vaccine or immunogenic composition of claim 12, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain EF10197 having an amino acid sequence of SEQ ID NO:
 11. 15. The vaccine or immunogenic composition of claim 12, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain WU2 having an amino acid sequence of SEQ ID NO:
 13. 16. The vaccine or immunogenic composition of claim 12, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain DBL5 having an amino acid sequence of SEQ ID NO:
 14. 17. The vaccine or immunogenic composition of claim 12, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain EF6796 having an amino acid sequence of SEQ ID NO:
 15. 18. The vaccine or immunogenic composition of claim 12, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain 0922134 having an amino acid sequence of SEQ ID NO:
 16. 19. The vaccine or immunogenic composition of claim 12, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain BG9163 having an amino acid sequence of SEQ ID NO:
 17. 20. The vaccine or immunogenic composition of claim 1, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from clade
 3. 21. The vaccine or immunogenic composition of claim 20, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA having an amino acid sequence of SEQ ID NO:
 18. 22. The vaccine or immunogenic composition of claim 20, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain AC122 having an amino acid sequence of SEQ ID NO:
 19. 23. The vaccine or immunogenic composition of claim 20, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain EF3296 having an amino acid sequence of SEQ ID NO:
 20. 24. The vaccine or immunogenic composition of claim 20, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain BG8090 having an amino acid sequence of SEQ ID NO:
 21. 25. The vaccine or immunogenic composition of claim 1, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from clade
 4. 26. The vaccine or immunogenic composition of claim 25, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA having an amino acid sequence of SEQ ID NO:
 22. 27. The vaccine or immunogenic composition of claim 25, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain BG11703 having an amino acid sequence of SEQ ID NO:
 23. 28. The vaccine or immunogenic composition of claim 25, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain BG7817 having an amino acid sequence of SEQ ID NO:
 24. 29. The vaccine or immunogenic composition of claim 25, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain EF5668 having an amino acid sequence of SEQ ID NO:
 25. 30. The vaccine or immunogenic composition of claim 25, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain BG7561 having an amino acid sequence of SEQ ID NO:
 26. 31. The vaccine or immunogenic composition of claim 1, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from clade
 5. 32. The vaccine or immunogenic composition of claim 31, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain ATCC6303 having an amino acid sequence of SEQ ID NO:
 27. 33. The vaccine or immunogenic composition of claim 1, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from clade
 6. 34. The vaccine or immunogenic composition of claim 33, wherein the composition comprises an isolated PspA or an isolated immunogenic fragment of PspA from strain BG6380 having an amino acid sequence of SEQ ID NO:
 28. 